Depends on what kind of money you have. Especially if you are going to run them hard though, replace the timing belt, water pump, and oil seals while they aren't in a car, much easier to do on the ground. As for power, learn the basics of auto performance, google it. More air and fuel in, more air out. In an ideal world you want to get a cold air intake, larger throttle body, high flow intake manifold, performance camshaft, header, and high flow exhaust system. You can reprogram the ECU to match performance mods and get even more power. Or, you can boost it with a turbo, but that's very involved.

In reality, just get on ebay, buy a cheap cold air intake, header, and muffler. That's how you can pick up the most power for $200 or so.

Sell it to someone who wants an A4. I don't see why this is so difficult. There's no huge advantage to mixing and matching parts from these two engines. Just decide which one you want to keep and sell the other...